SNU Compbio Lab
Bulletin of the Korean Chemical Society
- A benchmark study of machine learning methods for molecular electronic transition: Tree-based ensemble learning versus graph neural network TOP NEW
- Contribution of Counterion Entropy to the Salt-Induced Transition Between B-DNA and Z-DNA TOP NEW
- Conformational Sampling of Flexible Ligand-binding Protein Loops TOP NEW
- Structural Basis of Functional Conversion of a Floral Repressor to an Activator: A Molecular Dynamics Simulation Study TOP NEW
- Efficiency of Rotational Operators for Geometric Manipulation of Chain Molecules TOP NEW
Journal of Chemical Information and Modeling
- GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network TOP NEW
- GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential TOP NEW
- Prediction of Molecular Electronic Transitions Using Random Forests TOP NEW
- GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds TOP NEW
- GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors TOP NEW
- Evaluation of GalaxyDock Based on the Community Structure–Activity Resource 2013 and 2014 Benchmark Studies TOP NEW
- GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains TOP NEW
Journal of Chemical Theory and Computation
- Physics-Inspired Accuracy Estimator for Model-Docked Ligand Complexes TOP NEW
- GalaxyDock-DL: Protein-Ligand Docking by Global Optimization and Neural Network Energy TOP NEW
- Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies TOP NEW
- Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane TOP NEW
- Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy TOP NEW
- Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations TOP NEW
Journal of Computational Chemistry
- GalaxyDock2-HEME: protein-ligand docking for heme proteins TOP NEW
- Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design TOP NEW
- GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility TOP NEW
- GalaxyTongDock: Symmetric and asymmetric ab initio protein–protein docking web server with improved energy parameters TOP NEW
- GalaxyDock2: Protein–ligand docking using beta-complex and global optimization TOP NEW
- LigDockCSA: Protein–ligand docking using conformational space annealing TOP NEW
- Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller TOP NEW
- Using quaternions to calculate RMSD TOP NEW
- A kinematic view of loop closure TOP NEW
Journal of Computer-Aided Molecular Design
- GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking TOP NEW
- Absolute binding free energies for octa-acids and guests in SAMPL5 TOP NEW
- Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge TOP NEW
Journal of Molecular Biology
- GalaxySagittarius-AF: Predicting Targets for Drug-Like Compounds in the Extended Human 3D Proteome TOP NEW
- GalaxyDomDock: An ab initio domain–domain docking web server for multi-domain protein structure prediction TOP NEW
- Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology TOP NEW
Journal of Physical Chemistry B
- Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane TOP NEW
- Tribute to Ken A. Dill TOP NEW
- Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation TOP NEW
- Cooperativity and Specificity of Cys2His2 Zinc Finger Protein-DNA Interactions: A Molecular Dynamics Simulation Study TOP NEW
- Strength of Cα−H···O=C Hydrogen Bonds in Transmembrane Proteins TOP NEW
Methods in Molecular Biology
- Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server. In "Protein Structure Prediction" TOP NEW
- Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock. In "Modeling Peptide-Protein Interactions" TOP NEW
- Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers. In "Computational Design of Ligand Binding Proteins" TOP NEW
Nature Communications
- Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family TOP NEW
- Structural basis of neuropeptide Y signaling through Y1 receptor TOP NEW
- Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains TOP NEW
Nucleic Acids Research
- Discovery of highly active kynureninases for cancer immunotherapy through protein language model TOP NEW
- HProteome-BSite: predicted binding sites and ligands in human 3D proteome TOP NEW
- GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking TOP NEW
- GalaxyRefine2: Simultaneous refinement of inaccurate local regions and overall protein structure TOP NEW
- GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure TOP NEW
- Galaxy7TM: Flexible GPCR-ligand docking by structure refinement TOP NEW
- GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization TOP NEW
- GalaxySite: ligand-binding-site prediction by using molecular docking TOP NEW
- GalaxyRefine: protein structure refinement driven by side-chain repacking TOP NEW
- GalaxyWEB server for protein structure prediction and refinement TOP NEW
- The FALC-Loop web server for protein loop modeling TOP NEW
Proteins
- Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies TOP NEW
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment TOP NEW
- Protein oligomer structure prediction using GALAXY in CASP14 TOP NEW
- Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment TOP NEW
- Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges TOP NEW
- Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45 TOP NEW
- Prediction of protein oligomer structures using GALAXY in CASP13 TOP NEW
- Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment TOP NEW
- Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning TOP NEW
- Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment TOP NEW
- The challenge of modeling protein assemblies: the CASP12-CAPRI experiment TOP NEW
- Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30 TOP NEW
- Effective protein model structure refinement by loop modeling and overall relaxation TOP NEW
- Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment TOP NEW
- Blind prediction of interfacial water positions in CAPRI TOP NEW
- Community-wide evaluation of methods for predicting the effect of mutations on protein–protein interactions TOP NEW
- Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors TOP NEW
- New molecular interaction of IIANtr and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies TOP NEW
- Refinement of unreliable local regions in template-based protein models TOP NEW
- Refinement of protein termini in template-based modeling using conformational space annealing TOP NEW
- De novo protein structure prediction by dynamic fragment assembly and conformational space annealing TOP NEW
- Protein loop modeling by using fragment assembly and analytical loop closure TOP NEW
- A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect TOP NEW
others
ACS Catalysis
ACS Omega
Angewandte Chemie International Edition
- Switchable Nanoporous Sheets by the Aqueous Self-Assembly of Aromatic Macrobicycles TOP NEW
- Self-Dissociating Tubules from Helical Stacking of Noncovalent Macrocycles TOP NEW
BMC Bioinformatics
Biochemistry
Biodesign
- Accurate protein structure prediction: what comes next? TOP NEW
- Prediction of Protein Structure and Interaction by GALAXY Protein Modeling Programs TOP NEW
Bioinformatics
Biophysical Journal
Cell Reports
Cellular and Molecular Life Sciences
Chemical Science
Chemosphere
Communications Biology
Computational and Structural Biotechnology Journal
- Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction TOP NEW
- CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking TOP NEW
Current Opinion in Structural Biology
- Artificial Intelligence in Therapeutic Antibody Design: Advances and Future Prospects TOP NEW
- High-resolution protein–protein docking by global optimization: recent advances and future challenges TOP NEW
EMBO Journal
EMBO Molecular Medicine
European Journal of Medicinal Chemistry
Human Mutation
Inflammatory Bowel Diseases
International Journal of Quantum Chemistry
Journal of Biological Chemistry
- A pGpG-specific phosphodiesterase regulates cyclic di-GMP signaling in Vibrio cholerae TOP NEW
- Cell–cell adhesion in metazoans relies on evolutionarily conserved features of the α-catenin·β-catenin–binding interface TOP NEW
Journal of Chemical Physics
Journal of Cheminformatics
- Deep learning molecular interaction motifs from Receptor structure alone TOP NEW
- CSearch: chemical space search via virtual synthesis and global optimization TOP NEW
Journal of the Korean Physical Society
Molecular Biology
PLoS Computational Biology
PLoS ONE
Physical Chemistry Chemical Physics
Proceedings of the National Academy of Sciences
Protein Science
- Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif TOP NEW
- The flexibility in the proline ring couples to the protein backbone TOP NEW
Science
Scientific Reports
- An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 TOP NEW
- GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking TOP NEW
Structure
- Structural basis for Y2 receptor-mediated neuropeptide Y and peptide YY signaling TOP NEW
- Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System TOP NEW
bioRxiv
- SHARP: Generating Synthesizable Molecules via Fragment-based Hierarchical Action-space Reinforcement Learning for Pareto Optimization TOP NEW
- TITANiAN: Robust prediction of T-cell epitope immunogenicity using adversarial domain adaptation network TOP NEW